Wheat flour and flour-based baking mixes can harbor Shigatoxigenic E. coli (STEC) and have been implicated in several outbreaks of foodborne illnesses. Wheat flour and its subsidiary products can become contaminated prior to and during processing, yet no effective post-processing microbial control measures have been identified for these commodities. Rehydration of baking mixes may allow for growth of contaminating bacteria. Ampicillin and streptomycin resistant strains of STEC (O26, O121, and O157:H7) were developed and their behavior in cake batter was monitored under different storage conditions. The population of these STEC strains declined over time in a standard cake batter formulation, but increased rapidly in commercial cake batters. Microencapsulated pelargonic acid was evaluated as a means to prevent the growth of STEC O26, O121, and O157:H7 in commercial cake batter but was found to have no impact on the growth of these strains and is therefore not an effective control measure.